RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3261
(342 letters)
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 183 bits (468), Expect = 2e-56
Identities = 83/297 (27%), Positives = 129/297 (43%), Gaps = 33/297 (11%)
Query: 45 LIRNCMLELVGYLKSMTNFDRPSPRFVLYGEHGVGKSMALVYALQYAHENNYLLVHIPWV 104
L+R LEL LK + + RFVL GE G GKS+ L A+ YA ++++H+P
Sbjct: 2 LVREETLELTKKLKE-ADASKKVVRFVLTGERGSGKSVLLAQAMAYAFTQGWIVLHVPEA 60
Query: 105 LRWFAYPKEVSHSLTKEGMVDLNIDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPREKS 164
W + + G+ D + AA WL+ K N + L+ +L S++Y W RE +
Sbjct: 61 EDWVNGTTDYAPDPGNPGLYDQPMYAAAWLQKILKANEEVLK--KLKLSKDYKWLKREST 118
Query: 165 EANIPLAALIEHGITRVKYASDVVDVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCK 224
A L L GI K A DV ++ E+K S V VDG+N+ F ++ +
Sbjct: 119 PAGSTLLDLASLGINDPKSAWDVFQAVWKELKAQS--KAPPVLVAVDGFNALF-GPSDYR 175
Query: 225 PEDKSKVLPSRVTLTRSVINLVQ--SDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAG 282
D + P +TL R ++L+ +D+ NG +V AL+ R
Sbjct: 176 TPDFKPIHPHDLTLVRLFLDLLSGKNDFPNGGVVTALAATGVSNTPR------------- 222
Query: 283 FESIDPFVPIHVPELNDEEFHNLLNLYESKKWLQ----TSEGREEIAFLTKRVPQKM 335
PI VP L+ EE +L+ Y L E+++ L P ++
Sbjct: 223 --------PIRVPGLSKEEARSLMEYYADSGILLKKVDEELVDEKLSLLGNGNPGEL 271
>gnl|CDD|187761 cd09321, TDT_like_3, The Tellurite-resistance/Dicarboxylate
Transporter (TDT) family. The
Tellurite-resistance/Dicarboxylate Transporter (TDT)
family includes members from all three kingdoms, but
only three members of the family have been functionally
characterized: the TehA protein of E. coli functioning
as a tellurite-resistance uptake permease, the Mae1
protein of S. pombe functioning in the uptake of malate
and other dicarboxylates, and the sulfite efflux pump
(SSU1) of Saccharomyces cerevisiae. In plants, the
plasma membrane protein SLAC1 (Slow Anion
Channel-Associated 1), which is preferentially expressed
in guard cells, encodes a distant homolog of fungal and
bacterial dicarboxylate/malic acid transport proteins.
SLAC1 is essential in mediating stomatal responses to
physiological and stress stimuli. Members of the TDT
family exhibit 10 putative transmembrane a-helical
spanners (TMSs).
Length = 327
Score = 36.1 bits (84), Expect = 0.022
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 96 YLLVHIPWVLRWFAYPKEVSHSLT 119
+ ++ +PW+LRW YPKE L
Sbjct: 44 FFVLLVPWLLRWILYPKEALADLK 67
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 32.6 bits (75), Expect = 0.086
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 71 VLYGEHGVGKSMALVYALQYAHENNYLLVHIP 102
VL GE G GK+ L + + V P
Sbjct: 8 VLTGESGSGKTTLLRRLARQLPNRRVVYVEAP 39
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 29.9 bits (68), Expect = 2.1
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGKS---MALVYALQYAHENNYLLVHIPWV 104
EL L+ + RP +YG+ G GK+ ++ L+ A E+ + V +V
Sbjct: 26 ELAKALRPILRGSRP-SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYV 80
>gnl|CDD|239432 cd03316, MR_like, Mandelate racemase (MR)-like subfamily of the
enolase superfamily. Enzymes of this subgroup share
three conserved carboxylate ligands for the essential
divalent metal ion (usually Mg2+), two aspartates and a
glutamate, and conserved catalytic residues, a
Lys-X-Lys motif and a conserved histidine-aspartate
dyad. Members of the MR subgroup are mandelate racemase,
D-glucarate/L-idarate dehydratase (GlucD),
D-altronate/D-mannonate dehydratase , D-galactonate
dehydratase (GalD) , D-gluconate dehydratase (GlcD), and
L-rhamnonate dehydratase (RhamD).
Length = 357
Score = 29.5 bits (67), Expect = 2.4
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 9/56 (16%)
Query: 123 MVDLN-----IDAAMWLRHFQKQNTKWLEDPRLTTSQEYVWSPRE-KSEANIPLAA 172
MVD N +A R ++ + W E+P + + + ++P+AA
Sbjct: 193 MVDANGRWDLAEAIRLARALEEYDLFWFEEP---VPPDDLEGLARLRQATSVPIAA 245
>gnl|CDD|214914 smart00922, MR_MLE, Mandelate racemase / muconate lactonizing
enzyme, C-terminal domain. Mandelate racemase (MR) and
muconate lactonizing enzyme (MLE) are two bacterial
enzymes involved in aromatic acid catabolism. They
catalyze mechanistically distinct reactions yet they are
related at the level of their primary, quaternary
(homooctamer) and tertiary structures.. This entry
represents the C-terminal region of these proteins.
Length = 97
Score = 28.0 bits (63), Expect = 2.4
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 123 MVDLN-----IDAAMWLRHFQKQNTKWLEDP 148
MVD N +A L + +W+E+P
Sbjct: 49 MVDANGAWTAEEAIRALEALDELGLEWIEEP 79
>gnl|CDD|239311 cd03013, PRX5_like, Peroxiredoxin (PRX) family, PRX5-like
subfamily; members are similar to the human protein,
PRX5, a homodimeric TRX peroxidase, widely expressed in
tissues and found cellularly in mitochondria,
peroxisomes and the cytosol. The cellular location of
PRX5 suggests that it may have an important antioxidant
role in organelles that are major sources of reactive
oxygen species (ROS), as well as a role in the control
of signal transduction. PRX5 has been shown to reduce
hydrogen peroxide, alkyl hydroperoxides and
peroxynitrite. As with all other PRXs, the N-terminal
peroxidatic cysteine of PRX5 is oxidized into a sulfenic
acid intermediate upon reaction with peroxides. Human
PRX5 is able to resolve this intermediate by forming an
intramolecular disulfide bond with its C-terminal
cysteine (the resolving cysteine), which can then be
reduced by TRX, just like an atypical 2-cys PRX. This
resolving cysteine, however, is not conserved in other
members of the subfamily. In such cases, it is assumed
that the oxidized cysteine is directly resolved by an
external small-molecule or protein reductant, typical of
a 1-cys PRX. In the case of the H. influenza PRX5
hybrid, the resolving glutaredoxin domain is on the same
protein chain as PRX. PRX5 homodimers show an A-type
interface, similar to atypical 2-cys PRXs.
Length = 155
Score = 28.7 bits (65), Expect = 2.6
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 250 WNNGAIVLALSPRANLPDRRESHLPLYM-----LKKAGFESI------DPFV 290
+ +V+ P A P HLP Y+ LK G + + DPFV
Sbjct: 27 FKGKKVVIFGVPGAFTPTCSAQHLPGYVENADELKAKGVDEVICVSVNDPFV 78
>gnl|CDD|223479 COG0402, SsnA, Cytosine deaminase and related metal-dependent
hydrolases [Nucleotide transport and metabolism /
General function prediction only].
Length = 421
Score = 29.0 bits (65), Expect = 3.6
Identities = 41/232 (17%), Positives = 67/232 (28%), Gaps = 30/232 (12%)
Query: 82 MALVYALQYAHENNYLLVH---IPWVLRWFAYPKEVSHSLTKE-----GMVDLNIDAAMW 133
+ L + E+ L++ I + P + K G V+ +
Sbjct: 10 LLLTNDPEGRIEDGDLVIEDGKIVAIGANAEGPPDEEVIDAKGKLVLPGFVNAHTHLDQT 69
Query: 134 L---RHFQKQNTKWLEDPRLTTSQEYVWSPREKSEANIPLAA--LIEHGITRVKYASDVV 188
L +WLE R +E E A LA ++ +G T + DVV
Sbjct: 70 LLRGLADDLPLLEWLE--RYVWPREARLLTEEDLYARALLALLEMLRNGTTTARTHVDVV 127
Query: 189 DVLFTEIKKLSTEGVCRTFVCVDGYNSFFAEKTNCKPEDKSKVLPSRVTLTRSVINLVQS 248
+ + E R + + F D + T ++
Sbjct: 128 AESADAAFEAALEVGLRAVLGPVLQDVAF--------PDPGAETDEELEETEELLREAHG 179
Query: 249 DWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFESIDPFVPIHVPELNDE 300
G V+ L+P E L L + V IH+ E DE
Sbjct: 180 ---LGRDVVGLAPHFPYTVSPE---LLESLDEL-ARKYGLPVHIHLAETLDE 224
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 29.2 bits (66), Expect = 3.9
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 229 SKVLPSRVTLTRSVINLVQSDWNN-GAIVLALSPRANLPDRRESHLPLYMLKKAGFESID 287
S+ LPS + R V+ L Q+D+ + A+VL+++ D R L L +K+ GF I
Sbjct: 9 SRELPSCFSTHREVVALDQTDFTDVAAVVLSVA------DSRSGILAL--IKRTGF-GIP 59
Query: 288 PFVPIHVPELNDEEFHNLLN 307
FV E E ++
Sbjct: 60 VFVATEEEEEVPAEVLPRIS 79
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 28.3 bits (64), Expect = 4.4
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 52 ELVGYLKSMTNFDRPSPRFV-LYGEHGVGKSMALVYALQYAHENNYLLVHIP 102
EL+ L+ + RF+ L+GE G GKS L A A E +++P
Sbjct: 24 ELLAALRQL--AAGKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP 73
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 29.0 bits (65), Expect = 4.4
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 66 PSPRFV-LYGEHGVGKSMALVYALQYAHEN 94
P+P+ V +YG GVGK+ A L+ A +N
Sbjct: 84 PNPQHVIIYGPPGVGKTAAARLVLEEAKKN 113
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 27.9 bits (62), Expect = 5.6
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 65 RPSPRFVL-YGEHGVGKSMALVYALQ 89
P VL G G GK+ +L+ L
Sbjct: 21 SGGPPSVLLTGPSGTGKT-SLLRELL 45
>gnl|CDD|235228 PRK04155, PRK04155, chaperone protein HchA; Provisional.
Length = 287
Score = 27.7 bits (62), Expect = 9.7
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 270 ESHLPLYMLKKAGFE 284
E+ LP+Y L KAGFE
Sbjct: 78 ETLLPMYHLHKAGFE 92
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.410
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,429,199
Number of extensions: 1653508
Number of successful extensions: 1546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1542
Number of HSP's successfully gapped: 23
Length of query: 342
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 244
Effective length of database: 6,590,910
Effective search space: 1608182040
Effective search space used: 1608182040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)